Z01-HG00140-03 Updated 9/2001 The homeodomain family of transcription factors plays a fundamental role in a diverse set of functions that include body plan specification, pattern formation, and cell fate determination during metazoan development. Members of this family are characterized by a helix-turn-helix DNA-binding motif known as the homeodomain. Homeodomain proteins regulate various cellular processes by specifically binding to the transcriptional control region of a target gene. These proteins have been conserved across a diverse range of species, from yeast to human. A number of inherited human disorders are caused by mutations in homeodomain-containing proteins. Phylogenetic analysis of these proteins, whose sequences were aligned based on the three-dimensional structure of the homeodomain, was performed using a distance matrix approach. The homeodomain proteins segregate into six distinct classes, and this classification is consistent with the known functional and structural characteristics of these proteins. An ancestral sequence signature that accurately describes the unique sequence characteristics of each of these classes has been derived. The phylogenetic analyseis, coupled with the chromosomal location of these genes, has provided powerful clues as to how each of these classes arose from the ancestral homeodomain. One specific homeodomain protein, FOXC1, is implicated in Axenfeld-Rieger malformations. Patients with Axenfeld-Rieger malformations typically show a spectrum of ocular findings, including iris hypoplasia, a prominent Schwalbe line, iris adhesions, and goniodysgenesis. The most severe cases show elevated intraocular pressure, leading to the development of glaucoma. Five missense mutations of the FOXC1 protein were examined using homology model building techniques. Molecular modeling of the FOXC1 forkhead domain predicted that the missense mutations led only to slight structural perturbations of FOXC1, even though these mutations are involved in significant changes in expression level or the ability of FOXC1 to bind to DNA. This is in contrast to previous work performed by this group on PITX2, mutations in which lead to similar ocular phenotypes; mutations in the PITX2 lead to global structural rearrangements, which in turn result in loss of function. Work is continuing in this area to better-understand these eye-related mutations and their net effect on vision.